Laser-induced thermal therapy, which has many advantages including rapid operation, minimal damage and insignificant toxicity and side effects, is considered to be a promising non-invasive/minimally invasive therapeutic methodology, and it attracts much attention in recent years. In order to improve the therapeutic effects, researchers study various types of photothermal therapy agents (PTAs). Compared with inorganic nanomaterials, PTAs based on organic nanomaterials have superior biocompatibility and biodegradability, and they are more promising for clinical translation. As a result, PTAs based on organic nanomaterials has rapid development in recent years. In this review, the recent progress of several typical classes of organic photothermal nano-agents, including near-infrared dye-containing micelles, protein-based photothermal agents, porphysomes, and conjugated polymers, is introduced, and their individual advantages and shortcomings are introduced. At last, the challenges and future direction of this field also be discussed.